Partnerships have become a ubiquitous model for delivering global health research. Notwithstanding their contribution toward improving health outcomes, partnerships have been scrutinised for how they operate and criticised for perpetuating inequities between stakeholders in low- and middle-income countries and high-income countries. Guidance to inform fair partnership practice has proliferated in recent decades and the emerging movement to decolonise global health has brought momentum for change. Amidst this evolving context, this study sought to summarise the guidance for partnership practice and explore experiences of partnership from the perspective of stakeholders in four sub-Saharan African research institutions. A scoping review of principles and guidelines for global health research partnerships found considerable convergence on the domains considered to be important for partnerships to strive towards equity. There was also good coherence between the themes identified from this review and two similar reviews published just prior to this review being completed. Qualitative interviews with researchers and administrators at research institutions in four countries in anglophone eastern and southern Africa found that participants’ experiences of partnership with high-income country collaborators were wide-ranging. Guidelines for partnership provided good coverage of the domains considered to be the key determinants of a healthy partnership but were not used to inform partnership practice. Partnerships generated considerable benefits to sub-Saharan African stakeholders and there was some evidence to suggest that they were becoming more equitable. However, participants also continued to experience a range of well-documented inequities and reported new issues arising in situations in which their institution had been the prime recipient of grant funds. Theories of power provide a useful way to describe and explain some of the experiences reported by study participants. Literature on decolonising global health provides further insights and the momentum of the movement offers potential to achieve further progress towards more equitable research partnerships. Meanwhile, long-term support targeted towards individuals, institutions and national research systems remains essential to fulfil the potential of research led from sub-Saharan Africa.